We investigated the feasibility of i.v. BU, CY and etoposide (BUCYE), followed by auto-SCT (ASCT) in patients with newly diagnosed primary central nervous system lymphoma (PCNSL). The planned treatment consisted of induction chemotherapy with five cycles of high-dose MTX and two cycles of high-dose cytarabine followed by conditioning with BUCYE (BU 3.2 mg/m², day -7 to day -5; CY 50 mg/kg, day -3 to day -2 and etoposide 200 mg/m², twice a day, days -5 and -4) and then ASCT. Between May 2005 and November 2008, 11 consecutive PCNSL patients were treated. All patients completed the treatment as planned, with no cases of treatment-related death or veno-occlusive disease. After BUCYE and ASCT, 10 patients achieved complete response (CR) or unconfirmed CR (CRu). Two patients, one partial response and one CRu, received further whole-brain radiotherapy, with all achieving CR. At a median follow-up of 25.0 months (8.8-50.7 months), six patients had relapsed, with a median event-free interval of 15.0 months (95% confidence interval, 4.5-25.6 months). Median survival time was not reached yet with a 2-year survival rate of 88.9%. The current treatment was feasible with a favorable tolerance profile. However, further regimen optimization is necessary because of high relapse rate.